A lot of people not familiar with Thomas also don't realize Henry is let out of the tunnel in the following episode of the TV series. Many people think Henry really was bricked up for always, and always, and always. But the truth is that it was to teach Henry a lesson for letting his vanity cause significant problems for the entire island.

To expand on that point, Sir Topham Hatt isn't being cruel (though as you mentioned he's not exactly being nice either), he's punishing an engine for jeopardizing the entire railway and putting the livelihoods of all of the other engines and employees at risk. The main line is critical for the railway's operation, as without it, there's no Express, no access to branch lines, and no way to deliver goods and passengers. Without a railway, they'd be out of a job and possibly scrapped, a fate that most engines outside of Sodor meet. And in addition to that, the island of Sodor is heavily reliant on the railway to function and is a major employer in the region. The railway going under would cause economic havok for the whole island. Topham knows this and had to take drastic measures to teach Henry the error of his ways.